Should the questions which seek comparison of one aircraft with another, be posted on Aviation SE? If Yes, under which category? If no, why not?
As a concept these questions can be okay, but they have to kept as specific as possible. Saying (to steal your question from another comment) "how are 4th and 5th generation fighters different", is more broad than, "how do the radar sigantures of 4th and 5th generation fighters differ? Are 5th generations radar signatures bigger or smaller?", which is a fairly particular question. The second, more specific, question is preferred because it allows us to go into detail on a particular facet of the difference between the two aircraft.
Anyway, that part was well covered by Federico, what I really wanted to add on was this: If you keep your questions very specific it should become pretty obvious what categories you should use. The second example question posted above would use the tags *radar and *fighters most likely. I would highly recommend making your questions specific enough that it can take advantage of the tags that we currently have. I don't think adding a tag that simple says "plane comparison" (or something like that) would be a good idea.
Bottom line: Just make sure that you are comparing specific things between two airplanes, and then use the tag associated with that thing. That will probably produce the best result.
As said here when speaking about accidents, comparisons are not bad per-se, but, depending on which kind of comparison you do in your question and the kind of question you ask, it might end up being on-topic or too broad.